x86: quark: Avoid chicken and egg problem

If we convert to use driver model pci on quark, we will encounter
some chicken and egg problems like below:

- To enable PCIe root ports, we need program some registers on the
  message bus via pci bus. With driver model, the first time to
  access pci bus, the pci enumeration process will be triggered.
  But without first enabling PCIe root ports, pci enumeration
  just hangs when scanning PCIe root ports.
- Similar situation happens when trying to access GPIO from the
  PCIe enabling codes, as GPIO requires its block base address
  to be assigned via a pci configuration register in the bridge.

To avoid such dilemma, replace all pci calls in the quark codes
to use the local version which does not go through driver model.

Signed-off-by: Bin Meng <bmeng.cn@gmail.com>
Acked-by: Simon Glass <sjg@chromium.org>